Weekly global Tool Linting and Tests #25
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| name: Weekly global Tool Linting and Tests | |
| on: | |
| schedule: | |
| # Run at midnight every monday | |
| - cron: '0 0 * * 1' | |
| repository_dispatch: | |
| types: [run-all-tool-tests-command] | |
| env: | |
| GALAXY_FORK: galaxyproject | |
| GALAXY_BRANCH: release_24.1 | |
| MAX_CHUNKS: 40 | |
| jobs: | |
| setup: | |
| name: Setup cache and determine changed repositories | |
| if: ${{ github.repository_owner == 'Helmholtz-UFZ' }} | |
| runs-on: ubuntu-latest | |
| outputs: | |
| galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| fork: ${{ steps.get-fork-branch.outputs.fork }} | |
| branch: ${{ steps.get-fork-branch.outputs.branch }} | |
| repository-list: ${{ steps.discover.outputs.repository-list }} | |
| chunk-count: ${{ steps.discover.outputs.chunk-count }} | |
| chunk-list: ${{ steps.discover.outputs.chunk-list }} | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Add reaction | |
| if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
| uses: peter-evans/create-or-update-comment@v4 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| repository: ${{ github.event.client_payload.github.payload.repository.full_name }} | |
| comment-id: ${{ github.event.client_payload.github.payload.comment.id }} | |
| reactions: hooray | |
| - name: Set galaxy fork and branch | |
| id: get-fork-branch | |
| run: | | |
| TMP="${{ github.event.client_payload.slash_command.args.named.fork }}" | |
| echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT | |
| TMP="${{ github.event.client_payload.slash_command.args.named.branch }}" | |
| echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT | |
| - name: Determine latest commit in the Galaxy repo | |
| id: get-galaxy-sha | |
| run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }} | |
| # Install the `wheel` package so that when installing other packages which | |
| # are not available as wheels, pip will build a wheel for them, which can be cached. | |
| - name: Install wheel | |
| run: pip install wheel | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: discover | |
| with: | |
| create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }} | |
| galaxy-fork: ${{ steps.get-fork-branch.outputs.fork }} | |
| galaxy-branch: ${{ steps.get-fork-branch.outputs.branch }} | |
| max-chunks: ${{ env.MAX_CHUNKS }} | |
| python-version: ${{ matrix.python-version }} | |
| - name: Show repository list | |
| run: echo '${{ steps.discover.outputs.repository-list }}' | |
| - name: Show chunks | |
| run: | | |
| echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})' | |
| lint: | |
| name: Check for missing containers | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Planemo lint | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: lint | |
| with: | |
| mode: lint | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| tool-list: ${{ needs.setup.outputs.tool-list }} | |
| additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion | |
| - uses: actions/upload-artifact@v4 | |
| if: ${{ failure() }} | |
| with: | |
| name: 'Tool linting output' | |
| path: lint_report.txt | |
| test: | |
| name: Test tools | |
| # This job runs on Linux | |
| runs-on: ubuntu-latest | |
| needs: setup | |
| if: ${{ needs.setup.outputs.repository-list != '' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }} | |
| python-version: ['3.11'] | |
| services: | |
| postgres: | |
| image: postgres:11 | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: postgres | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| # checkout the repository | |
| # and use it as the current working directory | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Get number of CPU cores | |
| uses: SimenB/github-actions-cpu-cores@v2 | |
| id: cpu-cores | |
| - name: Clean dotnet folder for space | |
| run: rm -Rf /usr/share/dotnet | |
| # the following 2 steps are needed for testing the scripting tool | |
| - name: Install Apptainer's singularity | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| - name: Symlink singularity | |
| run: ln -s $(which apptainer) $(dirname apptainer)/singularity | |
| - name: Install containers | |
| run: | | |
| echo "${{ needs.setup.outputs.repository-list }}" > repository_list.txt | |
| if grep -q scripting repository_list.txt; then | |
| singularity pull --dir /tmp docker://continuumio/anaconda3 | |
| singularity pull --dir /tmp docker://rocker/tidyverse | |
| fi | |
| # Start OMERO | |
| - name: Start OMERO | |
| uses: sudo-bot/action-docker-compose@latest | |
| with: | |
| cli-args: "-f .github/omero-docker-compose.yml up -d" | |
| # Setup environment | |
| - name: Set up Python environment for omero-py | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11.0' | |
| # Upload a dummy dataset in OMERO | |
| - name: Install dependencies and upload a OMERO dummy dataset | |
| run: | | |
| echo "Waiting for OMERO to be ready..." | |
| sleep 60 | |
| pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl | |
| pip install omero-py==5.19.4 | |
| omero login -s localhost -u root -w omero -p 6064 | |
| PID=$(omero obj new Project name='test_prj') | |
| DID=$(omero obj new Dataset name='test_dts') | |
| omero obj new ProjectDatasetLink parent=$PID child=$DID | |
| omero import -d $DID .github/dummy-dts-omero | |
| echo "Created the dummy dataset into OMERO" | |
| # download or create large test data via script | |
| - name: Create test data | |
| run: | | |
| set -x | |
| pip install planemo > /dev/null | |
| echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt | |
| mapfile -t REPO_ARRAY < repository_list.txt | |
| planemo ci_find_tools --chunk_count "${{ needs.setup.outputs.chunk-count }}" --chunk "${{ matrix.chunk }}" --output tool_list_chunk.txt "${REPO_ARRAY[@]}" | |
| cat tool_list_chunk.txt | sed 's@/[^/]*$@@' | sort -i > repository_list_chunk.txt | |
| while read repo | |
| do | |
| echo "executing test-data.sh for $repo" | |
| if [ -x $repo/test-data.sh ]; then | |
| cd $repo | |
| ./test-data.sh | |
| fi | |
| done < repository_list_chunk.txt | |
| - name: Planemo test | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: test | |
| with: | |
| mode: test | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| galaxy-fork: ${{ needs.setup.outputs.fork }} | |
| galaxy-branch: ${{ needs.setup.outputs.branch }} | |
| additional-planemo-options: --docker_run_extra_arguments '--add-host=host.docker.internal:host-gateway' | |
| chunk: ${{ matrix.chunk }} | |
| chunk-count: ${{ needs.setup.outputs.chunk-count }} | |
| galaxy-slots: ${{ steps.cpu-cores.outputs.count }} | |
| # Limit each test to 15 minutes | |
| test_timeout: 900 | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: 'Tool test output ${{ matrix.chunk }}' | |
| path: upload | |
| # - combine the results of the test chunks (which will never fail due | |
| # to `|| true`) and create a global test report as json and html which | |
| # is provided as artifact | |
| # - check if any tool test actually failed (by lookup in the combined json) | |
| # and fail this step if this is the case | |
| combine_outputs: | |
| name: Combine chunked test results | |
| needs: [setup, test] | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| # This job runs on Linux | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| path: artifacts | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Combine outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: combine | |
| with: | |
| mode: combine | |
| html-report: true | |
| markdown-report: true | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY | |
| - name: Create URL to the run output | |
| if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
| id: vars | |
| run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT | |
| - name: Create comment | |
| if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }} | |
| uses: peter-evans/create-or-update-comment@v4 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| repository: ${{ github.event.client_payload.github.payload.repository.full_name }} | |
| issue-number: ${{ github.event.client_payload.github.payload.issue.number }} | |
| body: | | |
| Summary: | |
| ${{ steps.combine.outputs.statistics }} | |
| [Find all tool test results here][1] | |
| [1]: ${{ steps.vars.outputs.run-url }} | |
| - name: Check outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: check | |
| with: | |
| mode: check |